DNA Ladder

Falsification-first testing of hypotheses about DNA's open questions on real public data.

This repository is a monorepo with clear tracks: each research program lives under tracks/<name>/, while shared governance and negative results stay at the repo root.

Tracks

Track	Path	One-line focus
SE / LLPS	tracks/se_llps/	Super-enhancers, LLPS coactivators, G4/R-loop/constraint tests (mostly nulls)
TE / Alu–3D	tracks/te_alu_3d/	Rare Alu/SVA SNVs vs 3D contacts & activity (C1 desk template + scale protocol)

Shared across tracks:

• null_results/ — REJECT / INCONCLUSIVE / CLOSED filings (all tracks)
• CLAUDE.md — prime directive + protocol
• CONTRIBUTING.md — how to add experiments without breaking the ladder
• RESEARCH_DIRECTIONS.md — open directions (historical + current)
• PROJECT_HISTORICAL_BRIEF_v1.md — historical & scientific status brief v1.1 (both tracks; claim table; wet-lab NO-GO)

Why tracks (variant B)

• One repo → one place for collaboration, Issues, and null_results memory.
• Hard boundaries → SE/LLPS scripts do not accidentally reshape TE claims (and vice versa).
• Publishable desk artifacts for TE without shipping huge .hic / sealed holdout dumps.

Quick start

git clone https://github.com/sergeeey/-DNA-Ladder-.git
cd -- -DNA-Ladder-   # or whatever local folder name you use

Pick a track and read its README.md. Large input files are not committed — see each track's DATA.md.

Protocol (short)

1. L0 gate (Descriptive / Predictive / Causal)
2. Novelty check (null_results/ + literature)
3. Pre-register claim.md before results
4. Real public data only
5. File honest verdicts in null_results/ when REJECT / INCONCLUSIVE

License / collaboration

Open for experiment and critique. Prefer PRs that stay inside one track unless the change is shared governance.